Quantitative Mass Spectrometry-based Proteomics Reveals the

Mar 24, 2010 - A total of 516 proteins were quantified, comprising well-known classically secreted proteins, such as apolipoprotein E, several catheps...
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Quantitative Mass Spectrometry-based Proteomics Reveals the Dynamic Range of Primary Mouse Astrocyte Protein Secretion Todd M. Greco,† Steven H. Seeholzer,† Adrian Mak,† Lynn Spruce,† and Harry Ischiropoulos*,†,‡ Departments of Pediatrics and Pharmacology, The Children’s Hospital of Philadelphia Research Institute and The University of Pennsylvania Philadelphia, Pennsylvania 19104 Received February 12, 2010

Abstract: Growing appreciation for astrocytes as active participants in nervous system development, neurovascular metabolic coupling, and neurological disease progression has stimulated recent investigation into specific astrocyte-secreted proteins that may mediate these functions. The current work utilized SILAC-generated isotope reference proteomes to quantify relative protein abundances between the astrocyte proteome and secretome. Multidimensional GeLC-MS/MS analysis of astrocyte conditioned media and cell lysates resulted in the relative quantification of 516 proteins, 92 of which were greater than 1.5-fold enriched in astrocyte-conditioned media (ACM). Eighty of the ACM-enriched proteins had Nterminal signal peptides, comprising well-known classically secreted proteins, such as apolipoprotein E and SPARC, and several cathepsins that localize to endosomal/ lysosomal compartments. The remaining twelve ACMenriched proteins, such as vimentin, ferritins, and histones, lacked N-terminal signal peptides. Also, 47 proteins contained predicted N-terminal signal peptides but were not enriched in ACM (3 kDa) was obtained by 30fold concentration by ultrafiltration of ACM at 4 °C using CentriPrep Ultracel YM-3 filters (Millipore, Billerica, MA). Filtrates were then adjusted with protease inhibitors, 2 µg/mL aprotinin, 3.3 µg/mL bestatin, 3.3 µg/mL E-64, and aliquoted and stored at -80 °C. Cell pellets were lysed by homogenization in 50 mM HEPES-NaOH, pH 7.2, containing 50 mM NaCl, 1 mM EDTA, 1% Triton-X100, and protease inhibitors (as above), incubated on ice for 20 min, and centrifuged at 20 000× g for 20 min at 4 °C. Protein concentration of conditioned media and soluble lysates was determined by the Bradford method. Astrocyte Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC). SILAC labeling of primary astrocytes was used to generate isotope reference proteomes for both intracellular and extracellular proteomes. Astrocytes were cultured by the protocol described above, except for the modification of culture medium and culture flasks. Minimal essential media devoid of natural abundance lysine and leucine was supplemented as above and also repleted with the respective isotope-labeled amino acid analogs. In preparation for media conditioning, enriched astrocytes were seeded in T-175 flasks at 12.7 × 106 cells/plate (20 mL) in serum-containing heavy isotope medium. Forty-eight hours later, serum was withdrawn as described 2766

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technical notes

Quantitative Proteomics of the Astrocyte Secretome lation (+57 amu). Database searching was performed with the following parameters: precursor tolerance, 30 ppm; fragment tolerance, 1.0 amu; variable modification of methionine (+16 amu), and for SILAC experiments, variable modification of leucine (+7.017 amu) and lysine (+8.014 amu). The maximum number of variable modifications per instance and per peptide was 3 and 4, respectively. 13C isotope mass check was enabled. SEQUEST sequence-to-spectrum assignments were analyzed by Scaffold (Proteome Software, Portland, OR), the TransProteomic Pipeline (TPP ver. 4.0.2), or DTASelect (ver. 2.0). For all analyses, reverse database hits were used to control error rate at the peptide and protein level to less than 1%. The following command-line parameters were used for modeling and filtering of sequence-to-spectrum assignments by DTASelect: -s 100 -d 0.1 -Smn 7 -e CON_ --iso --sp --mass --ionstat --trypstat. Peptides were assembled into protein groups to satisfy rules of parsimony requiring at least two unique peptides. Census Quantitative Isotope Labeling Analysis. The isotope labeling feature of Census (ver. 1.44) was used for automated computation and filtering of extracted ion chromatograms and peptide ratios, respectively.32 Individual isotope extraction of SILAC pairs was performed with a mass tolerance of 30 ppm and atom percent excess of 0.98. Default values for filtering of peptide ratios were used, except an outlier p-value of 0.2 was selected. Proteins with 2 or more unique, quantified spectra were retained. Protein ratio calculation was repeated for additional sample sets and normalized ratios were obtained by dividing the two experimental conditions to obtain relative fold differences in protein abundance. These normalized protein ratios were utilized for downstream functional and statistical analyses. LC-MRM-MS/MS Analysis of SILAC Pairs. This approach was used to determine the degree of isotope incorporation into the astrocyte proteome and to validate SILAC ratios obtained by proteome-wide SILAC quantification. Data-independent analysis of light and heavy isotope-labeled peptides was conducted using a “pseudo-MRM” approach on an LTQ XL mass spectrometer (Thermofisher Scientific, San Jose, CA). The RP-LC gradient was identical to the method described above. The mass spectrometer was set to repetitively perform dataindependent MS2 acquisition on specific light and heavylabeled SILAC precursor masses selected empirically based on MS/MS spectra acquired in data-dependent experiments, which allowed the selection of optimal precursor-product ion transitions (e.g., prominent y-ions at an m/z greater than the precursor, which often represented N-terminal to Pro or C-terminal to Asp/Glu fragment). Between 4 and 8 precursor masses (2-4 SILAC pairs) were monitored in a single segment, with an isolation width of 3.0, normalized collision energy of 28, 2 microscans, and accumulation time and target value of 100 ms and 5e3, respectively. Xcalibur was used to reconstruct precursor-product ion chromatograms. SILAC peptide pair ratios were computed by area under the curve (AUC) measurements. MRM protein ratios were calculated as the average of four SILAC peptide ratios (two precursors per protein × two product ions per precursor). Western Blot Analysis. Protein concentration of ACM and cellular lysates were measured using the Bradford reagent (Biorad, Hercules, CA). Thirty micrograms of ACM or cellular lysates from two independent biological replicates were denatured in LDS (6X) sample buffer by heating at 70 °C for 10 min, then separated by 1D SDS-PAGE. Proteins were transferred to PVDF membranes (Millipore, Billerica, MA) at 20 V overnight

at 25 °C and then visualized with Ponceau S to verify equal protein loading. Ponceau S was destained briefly with 0.01 N NaOH, rinsed with water, and then incubated in blocking buffer (BBT; Odyssey blocking buffer mixed 1:1 with TBS) for 1 h at 25 °C. Membranes were then incubated with primary antibody (see “Chemicals and Reagents”) in blocking buffer adjusted to contain 0.1% Tween-20 (BBT-t) for 1 h at 25 °C. Membranes were then washed in TBS containing 0.1% Tween-20 (TBS-t) and incubated with appropriate secondary antibodies conjugated to Alexa Fluor 680 or Alexa Fluor 800 (1:15000, Invitrogen, Carlsbad, CA) for 1 h in BBT-t. Membranes were washed in TBS-t and visualized using the Odyssey Infrared Imaging system (Licor Biosciences, Lincoln, NE). Quantification was performed by densitometry using the Odyssey system software (ver. 2.1). Computational and Functional Gene Ontology Analysis. For computational analysis of classically secreted proteins, FASTA sequences were submitted to SignalP33 to predict proteins containing signal peptides, followed by TargetP34,35 to predict the localization (Extracellular, Mitochondria, Other). For prediction of nonconventionally secreted proteins, SecretomeP 2.022 was used. FatiGO36 provide gene ontology annotation. Statistical Analysis of Normalized Protein Ratios. Histograms were constructed and statistical analyses were performed using GraphPad Prism 5 (GraphPad Software, Inc., San Diego, CA). For brefeldin A experiments, significantly altered protein ratios were determined from large-scale protein profiling experiments using the complementary error function (erfc) within Microsoft Excel (see eq 1), which determines the probability that each individual protein ratio is not significantly different from the average protein ratio.37 The average ratio and other parameters (shown below) were calculated from a Gaussian least-squares nonlinear regression of the distribution of protein ratios. Gaussian fits were constructed using the normal distribution equation provided in GraphPad Prism with automatic outlier detection enabled.

{

|

}

p ) erfc |log(rp |r0)| √2((∆log rp)2 + (∆log r0)2 + σ2)

(1)

where ∆log rp ) 0.4343(∆rp/rp), ∆ log r0 ) 0.4343(∆r0/r0), rp and ∆rp ) protein abundance ratio and its associated error, r0 and ∆r0 ) average curve fit ratio and its associated error, and σ ) mean error of the background distribution.

Results and Discussion Generation and Characterization of Isotope-Coded Reference Proteomes (IRPs). Previous work established astrocytes as a viable model for the study of protein secretion under various culture conditions.19-21,38 To further understand and define the pathways of astrocyte protein secretion, we employed a modified SILAC approach in primary mouse astrocyte cultures. In this approach, isotope reference proteomes (IRPs) were generated in independent experiments and then added to samples collected from natural abundance culture conditions. This strategy has been previously used to uncover novel biomarkers and pharmacological targets for leukemias with MLL translocations.39 Importantly, no significant changes in preparation of enriched astrocyte cultures were performed as compared to our previous work,19 except for the addition of heavy-labeled [13C6-15N2]-lysine and [13C6-15N1]-leucine to meJournal of Proteome Research • Vol. 9, No. 5, 2010 2767

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dium that was devoid of their light isotope analogs. Mixed glial/ neuronal cortical cultures were established from cortices dissected from a total of 20 P1 neonatal CD-1 mice and maintained in heavy labeled medium from in vitro day 0 until the end of the experiment at day 20. At 11 days in vitro, cells were washed, trypsinized and combined into a single cell stock to establish enriched astrocyte cultures (>95%). After 48 h, astrocytes were changed to serum-free heavy isotope-containing media and remained without media change for an additional 7 days. No differences in rate of proliferation, gross morphology (by light microscopy), or cell viability were observed (data not shown). Astrocyte-conditioned media (ACM) was collected and concentrated, while adherent cells were collected and lysed. The heavy labeled ACM IRP yielded about 1.5 mg of protein, while the astrocyte lysate IRP yielded approximately 25 mg of protein. Data-dependent and -independent mass spectrometric analyses were performed on each IRP to determine the atom percent excess of stable isotope incorporation. Protein aliquots (25 µg) from each IRP were in-solution trypsin digested. Peptides (5 µg) were separated by reverse-phase LC and analyzed by either data-dependent MS/MS on an LTQ-Orbitrap or by a dataindependent “pseudo-MRM” approach on an LTQ mass spectrometer. For the former approach, 1085 and 2067 unique peptides were identified from ACM and lysate IRPs, respectively, with less than 1% of unique peptides containing a light leucine or lysine. Atom percent excess was quantified by Census, a software tool that provides automated reconstruction of light/heavy (SILAC) extracted ion chromatograms and computation of SILAC peptide ratios (see “Experimental Procedures”). For greater than 98% of the leucine and/or lysinecontaining peptides, the light component was below the limit of quantification. In contrast, vimentin was identified in ACM by 30 unique peptides and had three SILAC peptide pairs that could be quantified. As shown in Figure 2, extracted ion chromatograms from two of the SILAC peptide pairs, EEAESTLQSFR and DNLAEDIMR, resulted in SILAC ratios of 0.02 (1:50), corresponding to an estimated atom percent excess of about 98%. The level of isotope enrichment was also supported by data-independent mass spectrometric analysis. In these experiments, 16 SILAC peptide pairs were selected for MS/MS analysis (2 unique peptides from 4 ACM proteins and 4 cell lysate proteins). Precursor-product ion chromatograms for the 2 peptide pairs from GAPDH showed greater than 98% incorporation (data not shown), while for the remaining 14 peptides, the light component was not detected. Collectively, these data demonstrated that culturing primary mouse astrocytes in isotope-containing medium for 20 days in vitro achieved at least 98% incorporation for the majority of the intracellular and extracellular proteome. Previous SILAC studies conducted in primary neurons demonstrated a maximum of 80% incorporation.29 The difference in isotope incorporation between neurons and astrocytes likely resulted from the ability of P1 astrocytes to maintain their proliferative state when cultured under serum conditions. Primary astrocytes cultures established from 20 neonatal mouse brains, maintained in heavy isotope-containing media and conditioned for 7 days, generated isotope reference proteomes (IRPs) that yielded sufficient protein to conduct about 75 largescale relative quantitative experiments. Since the same IRP was used as an internal standard for all samples, variability intro2768

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Figure 2. Extracted ion chromatograms of vimentin peptides from ACM isotope reference proteome. Extracted ion chromatograms (XICs) were constructed by the Census quantitation tool with automatic thresholds for acceptance of light/heavy extracted ion chromatograms set at a correlation coefficient of 0.7 and outlier detection value of 0.2. XICs correspond to tryptic peptides assigned to vimentin, (A) EEAESTLQSFR and (B) DNLAEDIMR, which were identified in the ACM isotope reference proteome. Comparing linear regression analysis of XIC pairs show a light (gray trace) to heavy (black trace) ratio of 0.02, which approximates 98% isotopic enrichment. The time window over which the regression analysis was performed is indicated by the gray shaded rectangle. A small vertical line denotes the MS/MS event from which the peptide was identified and the XIC reconstructed.

duced due to culturing under heavy-labeled conditions is largely eliminated in the normalized protein abundance ratio. SILAC Quantitative Analysis of Brefeldin A-Induced Changes in Protein Abundance. As a proof-of-concept, IRPs were used to quantify alterations in the astrocyte proteome and secretome following treatment with brefeldin A (BFA), which blocks anterograde ER-to-Golgi vesicular transport at least in part via inhibition of the small GTPase, Arf1p, preventing COPI coat protein assembly on transport vesicles.40,41 BFA treatment was selected as a proof-of-concept for several reasons: (1) the inhibitory effects of BFA on classical, ER-to-Golgi protein secretion have been well-documented,40,41 (2) predictive capabilities of N-terminal signal peptides for classical protein secretion are specific and sensitive,33,35 and (3) the treatment conditions and effects of BFA on primary astrocyte cultures have been previously documented, which showed effective inhibition of classical protein secretion in astrocytes.38 Consistent with work by Lafon-Cazal et al., BFA exposure at 1 µg/ mL for 24 h did not significantly impair cell viability (data not shown). ACM and soluble intracellular protein lysates isolated from control and BFA-treated astrocytes (10 µg) were mixed with respective isotope reference proteomes at a 1:1 ratio, separated by SDS-PAGE, and digested in-gel with trypsin. Peptides (∼2.5 µg) from each gel slice were analyzed by LC-MS/MS using an LTQ-Orbitrap XL mass spectrometer. SEQUEST sequence-to-spectrum assignments were generated and probabilistic validation of peptides was performed

Quantitative Proteomics of the Astrocyte Secretome

technical notes hypothesis that each protein ratio was not significantly different from the mean curve fit ratio (see “Experimental Procedures”).

Figure 3. Brefeldin A-induced changes in relative protein abundance. Relative protein abundance ratios were calculated by normalizing protein ratios calculated in the BFA-treated astrocyte sample to the corresponding protein ratio from the control sample. Gaussian curve fit parameters; mean ratio (r0), standard deviation of the mean ratio (SD), and the background distribution (σ) were calculated for protein ratio distributions. (A) Individual log2 protein ratios from ACM (black; N ) 231) and cell lysates (gray; N ) 535) plotted in order of increasing relative abundance. (B) Histogram of BFA-induced changes in cell lysates as a function of log2 normalized protein ratio. Protein ratio distribution demonstrated good fit to the Gaussian curve (r0 ( SD ) 1.28 ( 0.01, σ ) 1.28). (C) Significantly altered cell lysate protein ratios (black) versus nonsignificant protein ratios (white) calculated using the complementary error function (p < 0.05) and Gaussian curve fit values. Scaling of the y-axis has been modified to emphasis the significantly altered (black) data points. (D) Histogram of BFA-induced changes in relative protein abundance of ACM proteins. Curve fit values for ACM protein ratios were r0 ( SD ) 1.97 ( 0.10, σ ) 1.75. (E) Significantly altered cell lysate protein ratios (black) versus nonsignificant ratios (white) calculated using the complementary error function (p < 0.05) and Gaussian curve fit values.

by PeptideProphet.42 Peptide assignments were filtered by probability to achieve an error rate of less than 1% and then analyzed by Census. In total, 231 and 535 normalized protein ratios (RatioBFA/RatioCtl) from ACM and cellular lysates were calculated, respectively (Figure 3A). Previous large-scale protein expression profiling studies have used different statistical approaches to identify proteins that exhibit differential expression or abundance.24,37 One approach, implemented by Li and colleagues in the ASAPRatio algorithm,37 modeled a best-fit Gaussian curve to the distribution of protein ratios and then computed the complementary error function to test the null

Using this approach, the distribution of cellular lysate protein ratios showed a good fit to the Gaussian curve and resulted in a mean curve fit ratio close to the expected 1:1 (1.28 ( 0.01) (Figure 3B). Statistical analysis identified 21 out of 535 proteins that were significantly altered due to BFA treatment (p < 0.05) (Figure 3C and Supplemental Table 1, Supporting Information). Proteins such as coatomer subunit beta and gamma as well as RAP guanine nucleotide exchange factor 2 were down-regulated due to BFA treatment (see Supplemental Table 1, Supporting Information). In contrast, the relative intracellular abundance of several classically secreted proteins was found significantly increased, including cathepsin L1 (9.4-fold), apolipoprotein E (21-fold), and thrombospondin-1 (28-fold). Also, the ATPbinding cassette subfamily A member 1 (ABCA1) was increased 5-fold, consistent with its functional relationship between apolipoprotein E lipidation and promotion of mature lipoparticle secretion from astrocytes43 as well as macrophages.44 Moreover, the glucose-regulated proteins, grp78 and grp94, were 3.4 ( 1.5-fold (p ) 0.06) and 2.32 ( 1.05-fold (p ) 0.25) increased after BFA treatment, respectively. Though these changes did not reach statistical significance (p > 0.05), upregulation of glucose-regulated proteins is a known consequence of ER stress and the unfolded protein response.45 The observation that BFA exposure induced only a modest upregulation of these glucose-regulated proteins, while robustly inhibiting classical protein secretion, provided evidence that the BFA treatment conditions were appropriate. Overall, the proteins identified as differentially expressed in the intracellular proteome due to BFA treatment were consistent with disruption of the classical ER-Golgi trafficking system, including downregulation of several vesicular transport proteins as well as increased abundance of classically secreted proteins, which likely resulted from their secretion being inhibited. Next, the concomitant BFA-induced protein abundance changes were assessed in ACM. In contrast to cellular lysate protein ratios, the distribution of ACM protein ratios deviated from normality (Figure 3D). This result was not unexpected given that a significant proportion of proteins identified in ACM contain an N-terminal signal peptide and would be potential targets of BFA-mediated inhibition. Although the curve-fit values derived from the ACM distribution exhibited a wider distribution about the mean (σ) than the cellular lysate distribution (compare Figure 3B vs 3D), the strong inhibitory effect of BFA on classical secretion permitted the identification of 55 proteins that were significantly decreased in ACM after BFA treatment (p < 0.05) (Figure 3E and Supplemental Table 2, Supporting Information). Significantly, 51 of these proteins possessed an N-terminal signal peptide. On the other hand, 49 signal peptide-containing proteins were not significantly inhibited after BFA treatment. Several possible reasons could account for this observation. Certain signal peptide-containing proteins, such as CD45 and cystic fibrosis transmembrane conductance regulator (CFTR),46-48 are secreted by Golgi- or COPII-independent mechanisms and would be unaffected by BFA treatment. Alternatively, not all luminal or integral membrane proteins (which possess signal peptides) may actively accumulate in conditioned media under these experimental conditions. Also, deviation of the protein ratio distribution from normality and larger distribution about the mean (σ) may have contributed to reduced sensitivity. This highlights a challenge for differential quantitative proteomic studies where a large Journal of Proteome Research • Vol. 9, No. 5, 2010 2769

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Figure 4. Quantification and validation of relative protein enrichment in ACM. (A) Histogram of 516 relative enrichment ratios, expressed as normalized log2 ratios of ACM relative to cell lysates. Positive values represent proteins that were enriched in ACM, while negative values represent proteins that were enriched in cell lysates. Protein ratios greater than 1.5-fold were considered significantly enriched in ACM. (B) Comparison of enrichment ratios from global SILAC MS analysis to abundance ratios for the same proteins calculated by targeted MRM-MS/MS analysis. Six proteins that ranged from -6 to +6 log2-fold enriched in ACM were selected for MRM-MS/MS analyses. A dashed linear line represents the ideal 1:1 correlation. (C) Protein ratios from (A) were grouped by subcellular localization. A protein ratio of 1.5-fold is indicated by the dashed horizontal line, while solid horizontal lines represent median relative enrichment ratios. (D) Protein aliquots (30 µg) from ACM and cellular lysates (two independent biological replicates) were analyzed by Western blot (WB) for selected proteins that spanned the ACM enrichment profile distribution in (A). For proteins with more than one significant band (apolipoprotein E and clusterin), individual bands within each lane were quantified and summed before enrichment ratios were calculated. Bar graphs compare the average enrichment ratio calculated from WB densitometry analysis (N ) 2) to the enrichment ratio calculated by SILAC. Error bars reflect ( SD. SILAC standard deviation based on individual SILAC peptide ratios (see values in Table 1 and Supplemental Table 3, Supporting Information). (D) Western blot analysis for apolipoprotein E, SPARC, and clusterin, which showed significant enrichment in ACM. (E) Western analysis for macrophage inhibitory factor (MIF) and cyclophilin B (peptidylprolyl isomerase B). Both have N-terminal signal peptides, but were not enriched in ACM. Enrichment ratios determined by WB for abundant cytosolic proteins, alpha-tubulin and GAPDH, were in agreement with SILAC analysis.

proportion of the proteome is significantly altered. For these cases, development and validation of more sophisticated statistical analyses will be useful for improving sensitivity and accuracy while maintaining low false discovery rates. Despite these drawbacks, the data support the use of SILAC-generated isotope reference proteomes as a tool for quantification of relative protein abundance within the astrocyte secretome and intracellular proteome. Protein Enrichment Profile of ACM from Naı¨ve Primary Astrocyte Cultures. Using this SILAC-based analysis, a quantitative protein enrichment profile of astrocyte conditioned media under basal culture conditions was constructed. The extent of protein enrichment in ACM was calculated by comparing the relative abundance ratios between the extracellular and intracellular compartments. For this purpose, a “whole cell” IRP was generated by mixing isotope-coded reference proteins from both the intracellular and extracellular proteomes. This “whole cell” IRP was then mixed with ACM and cell lysates samples obtained from the same astrocyte culture after 7 days of conditioning in light isotope media. 2770

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Equal aliquots (100 µg) of ACM and cell lysate samples were split between two lanes, resolved by SDS-PAGE, and digested in-gel with trypsin. Extracted peptides corresponding to gel slices from replicate lanes were pooled and analyzed by LC-MS/MS. SEQUEST sequence-to-spectrum assignments were processed by DTASelect49 for protein identification (see Supporting Information) and then by Census32 for quantitative analysis, resulting in the relative quantification of 516 proteins. Normalized protein ratios (RatioACM/RatioLysate) represent the fold difference in abundance between the extracellular and intracellular compartment. The distribution of protein enrichment ratios spanned at least 4 orders of magnitude (Figure 4A) and included cytosolic proteins such as filamins and ribosomal subunits that were 20- to 50-fold more abundant in cell lysates, as well as secreted proteins such as SPARC and alpha-2macroglobulin, which were 20- to 50-fold more abundant in ACM (see Supplemental Table 3, Supporting Information). An additional 109 protein were excluded from the ACM enrichment profile as their ratios were calculated to infinity (i.e., the calculated cellular lysate protein ratio was 0). At least a subset

technical notes

Quantitative Proteomics of the Astrocyte Secretome a

Table 1. Proteins with Significant Enrichment in ACM accession

protein name

ratiob

SDc

P08226 O09164 P10923 Q8R422 Q00493 P07214 A2APM1 P47867 Q3UGY5 Q6GQT1 P02463 O88307 P43025 P29533 Q921T4

Apolipoprotein E Extracellular superoxide dismutase [Cu-Zn] Osteopontin CD109 antigen Carboxypeptidase E SPARC CD44 antigen Secretogranin-3 Fibronectin 1 Alpha-2-macroglobulin-P Collagen alpha-1(IV) chain Sortilin-related receptor Tetranectin Vascular cell adhesion protein 1 Phospholipase A2, group VII (Platelet-activating factor acetylhydrolase, plasma) Tenascin Epididymal secretory protein E1 Insulin-like growth factor-binding protein-like 1 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 Glypican-4 Clusterin Growth arrest-specific protein 6 Cystatin-C Cadherin-13 Nucleobindin-1 Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 Ceruloplasmin Brevican core protein Plasma glutamate carboxypeptidase Peptidyl-prolyl cis-trans isomerase C Cathepsin S Complement component 3 Prolow-density lipoprotein receptor-related protein 1 Fat 1 cadherin (Fragment) Tissue alpha-L-fucosidase Neurocan core protein Pigment epithelium-derived factor Exostosin-like 2 Collagen alpha-1(XII) chain Neural cell adhesion molecule 1 Mammalian ependymin-related protein 1 Protein FAM3C Sulfhydryl oxidase 1 Cathepsin D Beta-mannosidase Serine protease inhibitor A3N N-acetylglucosamine-6-sulfatase Cell adhesion molecule 4 Plexin B2 (MCG140951) (Plxnb2 protein) Collagen alpha-1(VI) chain Complement C1q tumor necrosis factor-related protein 5 Alpha-N-acetylglucosaminidase (Sanfilippo disease IIIB) Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 DSD-1-proteoglycan Sulfated glycoprotein 1 Protein CREG1 N-glycan processing alpha-mannosidase IIx N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase Palmitoyl-protein thioesterase 1 Beta-hexosaminidase subunit beta Acid sphingomyelinase-like phosphodiesterase 3a Dipeptidyl-peptidase 2 Legumain Lysosome-associated membrane glycoprotein 2 Putative phospholipase B-like 2

414.00 327.00 187.25 76.00 74.33 67.00 65.33 64.00 57.67 45.60 41.89 31.45 30.62 30.15 29.70

244.00 50.00 93.50 22.50 26.33 35.93 4.33 16.00 87.06 28.62 12.13 5.76 5.62 4.23 4.80

38 15 4 50 46 36 3 29 119 140 9 42 8 21 43

/ / / / / / / / / / / / / / /

6 1 1 1 1 5 1 1 6 9 2 6 1 1 1

EM EM EM EM EM EM EM EM EM EM EM EM EM EM EM

27.30 22.00 21.33 18.40 16.91 15.71 14.67 14.00 13.27 12.29 12.13 12.00 11.23 10.37 10.36 10.09 9.75 9.48 9.40 8.56 8.47 7.65 7.50 7.25 7.00 7.00 6.81 5.88 5.25 5.03 5.02 4.92 3.83 3.79 3.76 3.55 3.50 3.44 3.22 3.04 2.95 2.94 2.88 2.79 2.78 2.77 2.70 2.60 2.55 2.43

10.10 12.65 2.83 3.02 17.02 12.44 2.33 2.45 2.27 2.22 2.33 14.40 2.39 1.74 0.57 2.09 11.25 4.78 1.52 1.73 10.22 9.26 0.38 16.12 1.71 1.76 3.28 1.08 8.52 1.31 2.23 1.18 0.50 7.13 0.68 0.35 0.47 0.64 4.07 0.72 0.71 0.60 2.13 0.41 1.77 0.36 0.66 0.57 1.53 0.58

10 19 14 20 34 62 26 37 5 22 6 37 14 10 4 18 130 99 64 8 47 34 3 109 10 13 5 27 42 5 20 18 9 19 12 11 16 14 25 29 5 3 15 17 32 8 9 16 5 14

/ / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /

1 7 1 2 2 6 1 1 1 6 2 2 2 2 2 1 5 22 2 2 2 3 1 4 1 10 2 1 8 1 2 4 1 13 1 2 7 2 3 13 2 2 6 12 4 3 4 1 4 10

EM EM EM ER EM EM EM EM EM EM G EM EM EM EM EL EM EM EM EL EM EM ER EM EM EM EM EM EL EL EM EL EM EM EM EM EL ER EM EM EM G EL EL EL EM EL EL EL EL

Q80YX1 Q9Z0J0 Q80W15 Q9R0E1 P51655 Q06890 Q61592 P21460 Q9WTR5 Q02819 Q3UHN9 Q61147 Q61361 Q9WVJ3 P30412 O70370 Q80XP1 Q91ZX7 Q9QXA3 Q99LJ1 P55066 P97298 Q9ES89 Q60847 P13595 Q99M71 Q91VU0 Q8BND5 P18242 Q8K2I4 Q91WP6 Q8BFR4 Q8R464 B2RXS4 Q04857 Q8K479 O88325 Q9R0B9 Q9WUT8 Q61207 O88668 Q197W7 Q64191 O88531 P20060 P70158 Q9ET22 O89017 P17047 Q3TCN2

pep countd

SLe

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Table 1. Continued accession

protein name

ratiob

SDc

A2ARV4 Q9EQH2 P10605 P50429 P01029 Q9WV54 Q91XG3 Q60648 P16675 Q07797 O09159 O54782 P23780 P97290 Q9WUU7 P20152 P62806 P27661 Q61599 Q3UCL5 Q61233 P09528 P00493 P80314 O88569 Q8CHQ7 P10852

Low-density lipoprotein receptor-related protein 2 Endoplasmic reticulum aminopeptidase 1 Cathepsin B Arylsulfatase B Complement C4-B Acid ceramidase Hexosaminidase A Ganglioside GM2 activator Lysosomal protective protein Galectin-3-binding protein Lysosomal alpha-mannosidase Epididymis-specific alpha-mannosidase Beta-galactosidase Plasma protease C1 inhibitor Cathepsin Z Vimentin Histone H4 Histone H2A.x Rho GDP-dissociation inhibitor 2 Ferritin Plastin-2 Ferritin heavy chain Hypoxanthine-guanine phosphoribosyltransferase T-complex protein 1 subunit beta Heterogeneous nuclear ribonucleoproteins A2/B1 UPF0727 protein C6orf115 homologue 4F2 cell-surface antigen heavy chain

2.24 2.20 2.16 2.12 2.03 1.96 1.93 1.87 1.87 1.78 1.69 1.64 1.55 1.54 1.53 27.43 16.17 6.82 4.80 3.75 3.75 3.59 2.63 2.40 2.06 2.01 1.48

0.62 0.57 1.34 0.72 0.77 0.36 1.36 0.40 0.73 0.22 0.21 0.89 0.38 1.53 0.48 19.36 4.64 1.93 2.56 0.79 1.04 1.25 0.60 0.39 0.65 0.01 0.34

pep countd

59 6 43 9 109 16 13 20 25 21 23 21 10 34 15 61 9 4 2 9 12 7 9 5 3 2 9

/ / / / / / / / / / / / / / / / / / / / / / / / / / /

SLe

9 3 13 3 1 7 3 6 12 1 1 4 1 2 3 8 7 6 2 1 2 2 6 2 2 2 2

EM ER EL EL EM EL EL EL EL EM EL EM EL EM EL O O O O O O O O O O O O

a Proteins are sorted in order of decreasing protein ratio, as well as by predicted classical and putative non-conventional section (designated by O in last column). b Protein ratio calculated from the intensity weighted average of individual peptide ratios. Ratio reflects the fold difference in protein abundance of ACM relative to cell lysates. c Standard deviation of the protein ratio, calculated by error propagation derived from individual peptide ratios for ACM and cell lysates. d Number of unique, quantified peptides used to calculate the protein ratio from ACM (left) and cell lysates (right) samples. A minimum of 2 unique, quantified peptides were required in at least ACM or cell lysates samples. e Predicted protein subcellular localization. Primary sequence analysis was performed by Signal P 3.0 to distinguish N-terminal signal peptide-containing proteins from nonsignal peptide-containing proteins (classified as cytosolic), followed by TargetP to provide predicted subcellular localization. EM, Extracellular/Plasma membrane; EL, Endo/Lysosome; G, Golgi; M, Mitochondria; ER, Endoplasmic reticulum; O, Cytoplasm/Nucleus/Other.

of these excluded proteins could be secreted since 75% possessed a signal peptide and all were confidently identified by isotope reference peptides in both samples. This suggests that their low intracellular abundance may have hindered quantification or that increased sample complexity in cellular lysates could have contributed to poor quantification, especially at low signal-to-noise. Next, MRM quantitative MS analysis was used to estimate the linear range of ACM enrichment ratios calculated by SILAC analysis, as it provides improved selectivity and sensitivity compared to nontargeted, global approaches based on precursor (MS1) ion abundance. Six proteins were selected, GAPDH, triosphosphate isomerase, glyoxylase domain-containing protein 4, alpha-N-acetylglucosaminidase, histone H4, and SPARC, which ranged in relative enrichment from -6 to +6 (log2 units). Light and heavy SILAC peptide pairs were selected empirically based on MS and MS/MS spectra from previous data-dependent experiments, facilitating the selection of optimal precursorproduct ion transitions. Light-to-heavy peptide ratios were calculated from data-independent acquisition of MS/MS spectra and reconstruction of precursor-product ion chromatograms by Xcalibur. MRM protein enrichment ratios were then calculated as the average ratio from two unique peptides and two distinct precursor-product ion transitions per peptide. As shown in figure 4B, SILAC enrichment ratios were in good agreement with targeted MRM ratios between -4 and +4 log2 units, while for ratios outside this range, enrichment ratios measured by SILAC were systematically greater than those 2772

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measured by MRM (Figure 4B). Furthermore, both global and targeted mass spectrometry-based determination of extracellular enrichment ratios were largely consistent with Western blot analyses of two independent biological replicates for classically secreted proteins, clusterin and cyclophilin B, as well as MIF, a nonconventional secreted protein, and two cytosolic proteins (GAPDH and alpha-tubulin) (Figure 4D and E). Relative enrichment measured by Western for the classically secreted proteins, apolipoprotein E and SPARC, were less than those calculated by SILAC (Figure 4C, top), which was not unexpected given that these ratios were likely outside the linear range of quantification (see Figure 4B, log2 ratio > 4). Examination of subcellular localization as a function of ACM enrichment revealed a significant clustering of enrichment ratios according to predicted localization, facilitating the identification of protein enrichment ratios that differed from the mean ratio within each subcellular compartment (Figure 4C). Proteins with a 1.5-fold or greater enrichment ratio were selected as significantly enriched in ACM (Table 1) as this represented two times the median of the relative standard deviation of enrichment ratios (RSD ) 25%; N ) 516). As expected, the extracellular/membrane protein group had the largest proportion of significantly enriched ratios (N ) 52/62; median ) 8.92-fold) (Figure 4C). These proteins also showed the widest range of enrichment ratios, consisting of constitutively secreted proteins with large (>50-fold) enrichment ratios such as extracellular superoxide dismutase and osteopontin, as well as secreted proteins with enrichment ratios less than

technical notes

Quantitative Proteomics of the Astrocyte Secretome one, such as mesencephalic astrocyte-derived neurotrophic factor/protein ARMET (0.32-fold) and gelsolin (0.48-fold) (see Supplemental Table 3, Supporting Information). Interestingly, gelsolin can exist in three different isoforms derived from alternative mRNA splicing.50,51 One isoform lacks a signal peptide and functions predominantly in the cytosol as an actinbinding protein. The other two isoforms are identical in sequence except for the addition of an N-terminal signal peptide. Upon secretion, these proteins retain their actinbinding ability and may function in actin filament clearance after tissue injury.50 This suggests that secreted proteins with enrichment ratios significantly less than one may have dual extra/intracellular function or could function in stimulusdependent, regulated secretory pathways. In the endosomal/lysosomal group (median enrichment ) 1.96-fold), 22 out of 31 proteins were significantly enriched (Table 1), including cathepsin B (2.2-fold), D (5.25-fold), S (10.1fold), and Z (1.5-fold), and beta-mannosidase (5.0-fold). Traditionally, possession of secretory lysosomes, which function primarily in immune defense, have been restricted to select cell types from the hematopoietic lineage (neutrophils, basophils, and cytotoxic T lymphocytes).52,53 Although astrocytes are not derived from this lineage, the participation of astrocytes in CNS immune responses has been well studied.13 Also, recent work has shown that cultured astrocytes spontaneously internalize styryl dyes into a lysosomal/endosomal vesicular pool, a subset of which undergo calcium-dependent exocytosis.54 In addition, astrocytic ATP release, which subserves calcium wave propagation1 and modulation of synaptic transmission55 was found to occur from a lysosomal vesicular pool.56 The median enrichment ratio for ER/Golgi/mitochondrialocalized proteins was 0.39-fold (N ) 31), while the remaining 392 proteins quantified did not contain N-terminal signal peptides and had a median enrichment ratio of 0.27-fold (Figure 4C). When analyzed by SecretomeP, a computational prediction algorithm for nonconventional protein secretion,22 160 proteins were predicted to be nonconventionally secreted including known nonconventionally secreted proteins such as galectins, macrophage migration inhibitory factor, and acylCoA-binding protein.57-60 A majority of these proteins (153) were less than 1.5-fold enriched in ACM, suggesting that under the current experimental conditions, nonconventional protein secretion did not significantly contribute to the overall abundance of astrocyte-secreted proteins quantified in ACM. Interestingly, 7 proteins, including vimentin (26-fold), and ferritin light (3.75-fold) and heavy (3.60-fold) chains were enriched in ACM (Table 1). MS/MS spectra and extracted ion chromatograms from selected proteins supported their identification and enrichment in ACM (see Supplemental Figure 1 and 2, Supporting Information). Vimentin has previously been characterized as a nonconventionally secreted protein from activated macrophages61 and also identified in astrocyte conditioned media by mass spectrometry-based proteomics.19 The secretion of ferritin chains has recently been documented in macrophages, which was shown to provide a functional ferritin-iron source for cultured erthyroid precursor.62 Although glial cells possess abundant ferritin and are able to accumulate iron, they lack transferrin receptors, which are thought to mediate much of brain-derived cellular import of iron.63 Therefore, additional investigation into the role of astrocytes in brain iron homeostasis may be warranted.

Conclusions Overall, this work demonstrated a SILAC-based quantitative mass spectrometry approach using isotope reference proteomes to quantify relative protein abundance changes within intracellular and extracellular astrocyte proteomes. The feasibility of SILAC quantitative MS for primary astrocytes was demonstrated by achieving stable isotope incorporation of 98% or greater at 20 days in vitro and by quantification of protein abundance changes within intracellular and extracellular proteomes after brefeldin A treatment. These IRPs were used to assemble a quantitative protein enrichment profile of astrocyteconditioned media collected from naı¨ve astrocyte cultures. In combination with computational prediction algorithms and subcellular localization, the enrichment profile of proteins in astrocyte conditioned media revealed a large dynamic range, comprising highly abundant classically secreted proteins, proteins that may proceed by nonconventional secretion, proteins that function in regulated secretion, as well as less abundant, cytosolic contaminants. Interestingly, the identification and quantification of potential lysosomal-secreted proteins provides new molecular targets to investigate the potential role of secretory lysosomes in astrocyte biology. While the function of lysosomal-secreted proteins from astrocytes is unclear, one could speculate that lysosomal enzymes may function in the extracellular space for tissue remodeling following cellular injury. This approach can be applied to comprehensively define, at the molecular level, basal and stimulated extracellular enrichment profiles under various experimental conditions, which will further advance our understanding of secretory pathways encompassing both classical as well as nonconventional secretion. Abbreviations: ACM, astrocyte-conditioned media; ALS, amyotrophic lateral sclerosis; CNS, central nervous system; GeLC-MS/MS, gel-liquid chromatography-tandem mass spectrometry; LC-MRM-MS/MS, liquid chromatography-multiple reaction monitoring-tandem mass spectrometry; NGF, nerve growth factor.

Acknowledgment. We thank Jessica Lee in the CHOP Protein Core for her assistance in operating and maintaining the mass spectrometers. We also thank Sung Kyu (Robin) Park for his technical assistance and continued development with the Census quantitative analysis software. The work was supported by grants from the National Institutes of Health NIA AG13966 and ES013508 NIEHS Center of Excellence in Environmental Toxicology. H.I. is the Gisela and Dennis Alter Research Professor of Pediatric Neonatology at the Children’s Hospital of Philadelphia Research Institute. Supporting Information Available: Table 1, a list of differentially expressed proteins in the astrocyte proteome after brefeldin A treatment; Table 2, a list of proteins with differential abundance in astrocyte-conditioned media after brefeldinA treatment; Table 3, a complete list of proteins identified and quantified in conditioned media of naı¨ve astrocytes; Figures 1 and 2, Representative MS/MS spectra and extracted ion chromatograms from selected nonconventionally secreted proteins; Excel file with total number of identified proteins, including unique and redundant peptides, from astrocyte-conditioned media and cellular lysates. This material is available free of charge via the Internet at http://pubs.acs.org. Journal of Proteome Research • Vol. 9, No. 5, 2010 2773

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